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. 2025 Jun 20;6(2):103769.
doi: 10.1016/j.xpro.2025.103769. Epub 2025 May 9.

Protocol to identify regulatory modules in Parkinson's disease progression using miRNA data and Boolean modeling

Ahmed Abdelmonem Hemedan  1 , Venkata Satagopam  2 , Reinhard Schneider  2 , Marek Ostaszewski  3
Affiliations

Protocol to identify regulatory modules in Parkinson's disease progression using miRNA data and Boolean modeling

Ahmed Abdelmonem Hemedan et al. STAR Protoc. .

Abstract

Regulatory modules are molecules that interact functionally, driving disease processes. Here, we present a protocol for identifying regulatory modules in Parkinson's disease (PD) using cohort-specific microRNA (miRNA) data and Boolean modeling. We describe steps for omics data collection, biomolecule and miRNA target analysis, and Boolean model construction and simulation. We then detail procedures for validation of the model and results. The modules identified using this protocol explain how miRNA-driven mechanisms influence PD progression in disease cohorts. For complete details on the use and execution of this protocol, please refer to Hemedan et al.1.

Keywords: Bioinformatics; Molecular Biology; Neuroscience; Systems biology.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

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References

    1. Hemedan A.A., Satagopam V., Schneider R., Ostaszewski M. Cohort-specific boolean models highlight different regulatory modules during Parkinson’s disease progression. iScience. 2024;27 doi: 10.1016/j.isci.2024.110956. - DOI - PMC - PubMed
    1. Marek K., Chowdhury S., Siderowf A., Lasch S., Coffey C.S., Caspell-Garcia C., Simuni T., Jennings D., Tanner C.M., Trojanowski J.Q., et al. The Parkinson’s progression markers initiative (PPMI) – establishing a PD biomarker cohort. Ann. Clin. Transl. Neurol. 2018;5:1460–1477. doi: 10.1002/acn3.644. - DOI - PMC - PubMed
    1. Stoll G., Caron B., Viara E., Dugourd A., Zinovyev A., Naldi A., Kroemer G., Barillot E., Calzone L. MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinformatics. 2017;33:2226–2228. doi: 10.1093/bioinformatics/btx123. - DOI - PubMed
    1. Funahashi A. In: Introduction to Systems Biology. David O’Connor, editor. Humana Press; 2007. CellDesigner: A Graphical Biological Network Editor and Workbench Interfacing Simulator; pp. 422–434.
    1. Gawron P., Ostaszewski M., Satagopam V., Gebel S., Mazein A., Kuzma M., Zorzan S., McGee F., Otjacques B., Balling R., Schneider R. MINERVA-a platform for visualization and curation of molecular interaction networks. NPJ Syst. Biol. Appl. 2016;2 - PMC - PubMed

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